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Deconstructing the Intercellular Interactome in Vascular Dementia with Focal Ischemia for Therapeutic Applications

GSE298799 Mus musculus (mouse) Single-nucleus RNA-seq 77 samples Submitted 2025/07/07 Platform GPL34290
At a glance

Single-nucleus RNA-seq · mouse · 77 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
77 samples: 11 conditions, mostly with about 6 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Deconstructing the intercellular interactome in vascular dementia with focal ischemia for therapeutic applicationsCell · 2025
Summary (written by the submitters)
Vascular dementia (VaD), the second-leading cause of dementia, is primarily a white matter ischemic disease with no direct therapies. Cell-cell interactions within lesion sites dictate disease progression or repair. To elucidate key intercellular pathways, we employed a VaD mouse model with focal ischemia replicating many elements of the complex pathophysiology of human VaD, combined with transcriptomic and functional analyses.
Read the full summary ↓
Integrating cell-type-specific mouse VaD transcriptomes and human VaD snRNA-Seq data, plus a custom ligand-receptor database (4,053 human and 2,032 mouse pairs), conserved dysregulated intercellular pathways in both species were identified. We demonstrate that two intercellular signaling systems, Serpine2-Lrp1 and CD39-A3AR, are disrupted in VaD. Reduced Serpine2 expression enhances oligodendrocyte progenitor cell (OPC) differentiation, promoting repair, while an A3AR-specific agonist—currently in clinical trials for psoriasis—restores tissue integrity and behavioral function in the VaD model. This study reveals intercellular signaling targets and provides a foundation for developing innovative therapies for VaD.
Published in
Deconstructing the intercellular interactome in vascular dementia with focal ischemia for therapeutic applications
Tian M, Kawaguchi R, Shen Y et al. · Cell 2025 · PMID 40592323 · doi:10.1016/j.cell.2025.06.002
This dataset
Open GSE298799 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE298799_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1271325 and SRA study SRP589506. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40592323) ↗
Study design
11 conditions, mostly with about 6 replicates each
mouse cerebral white matter microglia P2 str… ×9 mouse cerebral white matter microglia P4 str… ×9 mouse cerebral white matter pericyte stroke ×8 mouse cerebral white matter microglia P2 con… ×8 mouse cerebral white matter EC stroke ×7 mouse cerebral white matter pericyte control ×7 mouse cerebral white matter OPC control ×6 mouse cerebral white matter OPC stroke ×6 +3 more

Supports a between-group comparison across 77 samples.

How we read this: 11 replicated groups read from 77 sample titles; they account for 77 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 37 more — browse all 77 samples with per-sample file links →

Datasets on a similar topic

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